brmsfamily: Special Family Functions for 'brms' Models

Description Usage Arguments Details See Also Examples

View source: R/families.R

Description

Family objects provide a convenient way to specify the details of the models used by many model fitting functions. The family functions presented here are for use with brms only and will **not** work with other model fitting functions such as glm or glmer. However, the standard family functions as described in family will work with brms. You can also specify custom families for use in brms with the custom_family function.

Usage

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brmsfamily(
  family,
  link = NULL,
  link_sigma = "log",
  link_shape = "log",
  link_nu = "logm1",
  link_phi = "log",
  link_kappa = "log",
  link_beta = "log",
  link_zi = "logit",
  link_hu = "logit",
  link_zoi = "logit",
  link_coi = "logit",
  link_disc = "log",
  link_bs = "log",
  link_ndt = "log",
  link_bias = "logit",
  link_xi = "log1p",
  link_alpha = "identity",
  link_quantile = "logit",
  threshold = "flexible",
  refcat = NULL,
  bhaz = NULL
)

student(link = "identity", link_sigma = "log", link_nu = "logm1")

bernoulli(link = "logit")

negbinomial(link = "log", link_shape = "log")

geometric(link = "log")

lognormal(link = "identity", link_sigma = "log")

shifted_lognormal(link = "identity", link_sigma = "log", link_ndt = "log")

skew_normal(link = "identity", link_sigma = "log", link_alpha = "identity")

exponential(link = "log")

weibull(link = "log", link_shape = "log")

frechet(link = "log", link_nu = "logm1")

gen_extreme_value(link = "identity", link_sigma = "log", link_xi = "log1p")

exgaussian(link = "identity", link_sigma = "log", link_beta = "log")

wiener(
  link = "identity",
  link_bs = "log",
  link_ndt = "log",
  link_bias = "logit"
)

Beta(link = "logit", link_phi = "log")

dirichlet(link = "logit", link_phi = "log", refcat = NULL)

von_mises(link = "tan_half", link_kappa = "log")

asym_laplace(link = "identity", link_sigma = "log", link_quantile = "logit")

cox(link = "log", bhaz = NULL)

hurdle_poisson(link = "log")

hurdle_negbinomial(link = "log", link_shape = "log", link_hu = "logit")

hurdle_gamma(link = "log", link_shape = "log", link_hu = "logit")

hurdle_lognormal(link = "identity", link_sigma = "log", link_hu = "logit")

zero_inflated_beta(link = "logit", link_phi = "log", link_zi = "logit")

zero_one_inflated_beta(
  link = "logit",
  link_phi = "log",
  link_zoi = "logit",
  link_coi = "logit"
)

zero_inflated_poisson(link = "log", link_zi = "logit")

zero_inflated_negbinomial(link = "log", link_shape = "log", link_zi = "logit")

zero_inflated_binomial(link = "logit", link_zi = "logit")

categorical(link = "logit", refcat = NULL)

multinomial(link = "logit", refcat = NULL)

cumulative(link = "logit", link_disc = "log", threshold = "flexible")

sratio(link = "logit", link_disc = "log", threshold = "flexible")

cratio(link = "logit", link_disc = "log", threshold = "flexible")

acat(link = "logit", link_disc = "log", threshold = "flexible")

Arguments

family

A character string naming the distribution of the response variable be used in the model. Currently, the following families are supported: gaussian, student, binomial, bernoulli, poisson, negbinomial, geometric, Gamma, skew_normal, lognormal, shifted_lognormal, exgaussian, wiener, inverse.gaussian, exponential, weibull, frechet, Beta, dirichlet, von_mises, asym_laplace, gen_extreme_value, categorical, multinomial, cumulative, cratio, sratio, acat, hurdle_poisson, hurdle_negbinomial, hurdle_gamma, hurdle_lognormal, zero_inflated_binomial, zero_inflated_beta, zero_inflated_negbinomial, zero_inflated_poisson, and zero_one_inflated_beta.

link

A specification for the model link function. This can be a name/expression or character string. See the 'Details' section for more information on link functions supported by each family.

link_sigma

Link of auxiliary parameter sigma if being predicted.

link_shape

Link of auxiliary parameter shape if being predicted.

link_nu

Link of auxiliary parameter nu if being predicted.

link_phi

Link of auxiliary parameter phi if being predicted.

link_kappa

Link of auxiliary parameter kappa if being predicted.

link_beta

Link of auxiliary parameter beta if being predicted.

link_zi

Link of auxiliary parameter zi if being predicted.

link_hu

Link of auxiliary parameter hu if being predicted.

link_zoi

Link of auxiliary parameter zoi if being predicted.

link_coi

Link of auxiliary parameter coi if being predicted.

link_disc

Link of auxiliary parameter disc if being predicted.

link_bs

Link of auxiliary parameter bs if being predicted.

link_ndt

Link of auxiliary parameter ndt if being predicted.

link_bias

Link of auxiliary parameter bias if being predicted.

link_xi

Link of auxiliary parameter xi if being predicted.

link_alpha

Link of auxiliary parameter alpha if being predicted.

link_quantile

Link of auxiliary parameter quantile if being predicted.

threshold

A character string indicating the type of thresholds (i.e. intercepts) used in an ordinal model. "flexible" provides the standard unstructured thresholds, "equidistant" restricts the distance between consecutive thresholds to the same value, and "sum_to_zero" ensures the thresholds sum to zero.

refcat

Optional name of the reference response category used in categorical, multinomial, and dirichlet models. If NULL (the default), the first category is used as the reference. If NA, all categories will be predicted, which requires strong priors or carefully specified predictor terms in order to lead to an identified model.

bhaz

Currently for experimental purposes only.

Details

Below, we list common use cases for the different families. This list is not ment to be exhaustive.

Below, we list all possible links for each family. The first link mentioned for each family is the default.

Please note that when calling the Gamma family function of the stats package, the default link will be inverse instead of log although the latter is the default in brms. Also, when using the family functions gaussian, binomial, poisson, and Gamma of the stats package (see family), special link functions such as softplus or cauchit won't work. In this case, you have to use brmsfamily to specify the family with corresponding link function.

See Also

brm, family, customfamily

Examples

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 # create a family object
 (fam1 <- student("log"))
 # alternatively use the brmsfamily function
 (fam2 <- brmsfamily("student", "log"))
 # both leads to the same object
 identical(fam1, fam2) 

brms documentation built on March 14, 2021, 5:06 p.m.